This glyph draws a section of a chromosome ideogram. It relies on certain data from the feature to determine which color should be used (stain) and whether the segment is a telomere or centromere or a regular cytoband. The centromeres and 'var'-marked bands are rendered with diagonal black-on-white patterns if the "-patterns" option is true, otherwise they are rendered in dark gray. This is to prevent a libgd2 crash on certain 64-bit platforms when rendering patterned images.

The cytobandband features would typically be formatted like this in GFF3:

This is saying to use "white" for features whose stain attribute is "gneg", "silver" for those whose stain attribute is "gpos25", and so on. Several special values are recognized: "stalk" draws a narrower gray region and is usually used to indicate an acrocentric stalk. "var" creates a diagonal black-on-white pattern. "cen" draws a centromere.

If -bgcolor is just a color name, like "yellow", the glyph will ignore all bands and just draw a filled in chromosome.

If -bgfallback is set to a color name or value, then the glyph will fall back to the indicated background color if the chromosome contains no bands.

The following short script can be used to convert a UCSC cytoband annotation file into GFF format. If you have the lynx web-browser installed you can call it like this in order to download and convert the data in a single operation:

Otherwise you will need to download the file first. Note the difference between this script and input data from previous versions of ideogram.pm: UCSC annotations are used in place of NCBI annotations.